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Research Themes Protein design

Design and Discovery: Evolutionary Dynamics

SBKB [doi:10.1038/sbkb.2012.178]
Featured Article - January 2014
Short description: Differential dynamics in the dihydrofolate reductase family reveal how the enzyme has evolved to function in various cellular environments.

Alignment of E. coli (purple) and human (orange) DHFR at the three regions related to protein motions and dynamic mechanism. Red spheres represent the anchor residues for sequence alignment, with numbering from E. coli
DHFR. 1

In addition to structure, dynamics and flexibility are important in protein function. In fact, evolutionary pressure on protein dynamics could present a mechanism to fine-tune function. Wright and colleagues (PSI JCSG) investigated the dynamics of divergent members of the dihydrofolate reductase (DHFR) family and whether those features could account for the different kinetic properties of enzymes.

DHFR catalyzes the reduction of dihydrofolate to tetrahydrofolate (THF) via the oxidation of NADPH to NADP+. Although similar in structure, human and Escherichia coli DHFR orthologs differ in amino acid sequence and kinetic properties so drastically that human DHFR cannot rescue deletion of the DHFR gene in E. coli.

In the E. coli DHFR, slow dynamics (millisecond timescale) of an active site loop contributes to ligand flux and catalysis. Using NMR data and crystal structures, the authors determined that the corresponding loop in human DHFR is locked into a single conformation. Instead of loop dynamics, human DHFR facilitates ligand flux via a rigid-body hinging motion of two subdomains. By examining sequences of DHFR enzymes from different species, the authors were able to correlate the length of three regions (one loop and two hinges) to flexibility in the protein.

The authors speculate that DHFR has evolved different dynamics to function in different cellular environments. The concentrations of the products THF and NADP+ are higher in E. coli than in vertebrate cells, and the dynamics of the active site loop may enable the enzyme to avoid end-product inhibition. In contrast, the high concentration of NADPH in vertebrate cells should facilitate the oxidation to NADP+. To validate this hypothesis, the authors showed that human DHFR was more sensitive to end-product inhibition by NADP+ at concentrations similar to those found in E. coli. Furthermore, stabilizing mutations in the active site loop of E. coli DHFR that lock the loop in the closed conformation rendered the enzyme susceptible to end-product inhibition by NADP+.

These data demonstrate how proteins can evolve different dynamic mechanisms, while maintaining their three-dimensional fold, to function within a specific cellular environment.

Jennifer Cable

References

  1. G. Bhabha et al. Divergent evolution of protein conformational dynamics in dihydrofolate reductase.
    Nat. Struct. Mol. Biol. 20, 1243-1249 (2013). doi:10.1038/nsmb.2676

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